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Cancer staging statistics 8

The below statistics were taken from the cancer_staging_consolidated LabKey table from the Main Programme V8 data release. The table is built from the participant IDs and Tumour Sample Plate-key IDs from the cancer_analysis table which comprises QC-passed and interpreted tumour-normal genome pairs.

Completion as a percent of samples in the cancer_analysis table

This table shows the rate of data completion as a percentage of the total number of distinct participants and distinct tumour sample plate-keys in the cancer_analysis table vs the cancer_staging_consolidated table. Please note that this indicates the number of entries (participants or tumour sample plate-keys, respectively) for which we have stage information from one of the three input sources (cancer_participant_tumour, av_tumour, sact) within 12 months of acquiring the tumour sample. No additional checks were conducted.

# cancer_analysis cancer_staging_consolidated % complete
Distinct Participants 14,834 9,407 63.42
Distinct Tumour Sample Plate-keys 15,838 9,891 (number of rows in cancer_staging_consolidated table) 62.45

Completion rates of cancer_staging_consolidated by each source of staging

This table shows the number and rate of completion of tumour_sample plate-keys (n = 9,891) that are linked each of the three sources of staging. Note the link must be within a year of the tumour_clinical_sample_time field from the cancer_analysis table.

Source Number of tumour sample plate-keys % complete
av_tumour 7,325 74.06
cancer_participant_tumour 5,681 57.44
sact** 1,649 16.67

Summary and Distribution of time-difference days between tumour clinical sample time and staging information

This table shows the summary statistics of the distribution of time (in days) between the tumour_clinical_sample_time and the date of staging data acquisition. This is broken down by the three sources of staging.

NB: Note that in the below table and histogram, positive values indicate that the date of staging data acquisition is before the tumour_clinical_sample_time. Negative values indicate that the date of staging data acquisition is after the tumour_clinical_sample_time.

Stat cancer_participant_tumour av_tumour sact
minimum -365 -255 -365
q1 0 21 -59
median 16 42 -41
mean 31.55 67.36 -1.32
q3 48 87 49
maximum 365 365 365
NA 4,210 2,566 8,242

The below histograms show the same data but as a frequency distribution.

Frequency of the nearest staging source to the tumour clinical sample time for each tumour sample plate-key

The below table shows the break down of the tumour_sample plate-keys (n = 9,891) by the nearest source of staging data. For example if a tumour_sample plate-key has both linked av_tumour and sact staging entries, then the nearest entry to the tumour_clinical_sample_time is taken.

Staging Source Frequency
cancer_participant_tumour 5,024
av_tumour 4,167
sact 700

Frequency of breakdown by combination of data sources for each tumour sample plate-key

This table shows the frequency breakdown of the three sources of staging data across the tumour_sample plate-keys (n = 9,891). For example, if a tumour_sample plate-key has only cancer_participant_tumour and sact data available, then these two data sources are marked as Y.

cancer_participant_tumour av_tumour sact Frequency
N Y N 3,238
Y Y N 2,634
Y N N 2,370
N Y Y 797
Y Y Y 656
N N Y 175
Y N Y 21